Thursday, April 20, 2017

The last molecular evolution exam: Question #5

Many people believe that recombination evolved because it increases genetic variation in a population and this provided a selective advantage over species that didn’t have recombination. Do you agree with this explanation for the evolution of recombination? Why, or why not? What are the other possibilities?

14 comments
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It evolved because the dumb luck god has magical mystery powers and it knew in its 100% lack of wisdom that populations would die out long before Lady Luck could poof out a sufficient number of copying errors to make good things happen. See dumb luck god made a kind of crutch for naturalism by inserting all kinds of dynamic, non-random, regulated and otherwise intelligent mechanisms within individuals that, if not known about or admitted to (think hgt/epigenetics etc) could be misconstrued and lied about by scientists and then passed off as "evolution" This comes in handy when individual organisms in the field seem to change adaptively within their surroundings. Dumb luck god also knew how many people could be tricked into believing that "only populations evolve" when in reality individuals have a suite of mechanisms, including recombination, to help them adapt to the environment. Dumb luck god is still tricking people today that RMNS does anything in the way of animal-building.

"Genetic variation" seems to be a poorly defined term in the question. Does genetic variation refer to the mixing of alleles from the two haploid copies from both paretns? Does it refer to the new mixtures of alleles in germline cells produced during meiosis?

I would say that sexual recombination has the advantage of separating detrimental alleles from beneficial alleles. This reduces the accumulation of deleterious mutations, often called Muller's Ratchet. No longer does natural selection work at the level of the whole genome. Rather, natural selection can work at the level of the allele.

None of my students were confused about the meaning, and the potential causes, of genetic variation. They also know that diploidy and meiosis are effective ways of reducing the effects of Mueller's Ratchet. They also know that simply increasing the number of chromosomes can work almost as well as recombination.

You need to be precise in your definition of recombination in the exam question if what you mean is crossing over between parental alleles in meiosis. If you mean recombination in the sense of the molecular activity of RecA/Rad51 and similar molecules, then there are no species that do not have recombination. The distinction matters in this context if the fundamental role of recombination is to restore the correct topology to collapsed replication forks, with this biochemical activity later exploited to identify parental alleles thereby allowing reductive meiotic division and enabling sexual reproduction.

Recombination makes sense after selection. Since advantageous traits can come from different kinds of mutations, it makes sense that independent mutations would be recombined. Some experiments in directed evolution (90s), showed that the combination of selection, recombination speeded up, several-fold, the evolution of new specificity (from beta-lactams to cefotaxime, I think).

While there is no doubt regarding the impact of recombination on selection, I believe the question is directed more towards the origination of recombination. Professor Moran, what is your opinion regarding Cavalier-smith's review on this topic titled "Origins of the machinery of recombination and sex"?

No, I don't think that increasing genetic variation in a population and thus providing a selective advantage over species that don’t have recombination could be the be the explanation for the original evolution of recombination. That explanation is too far "downstream." Evolution happens generation by generation. At least at the start, the process has to provide an advantage (in survival or reproduction) to the individuals that have it.

I hypothesize that it could have started as a DNA repair mechanism. (Answer is very generalized; it's been a long time since I studied DNA in much detail.) DNA is long and can break. The broken ends are active and can reattach, but may not attach in the right place. Anything that would tend to control where reattachment happens would help the cell survive and reproduce. Mechanisms to break and reseal DNA help untwist it when it's in knots, and at this point are necessary for DNA replication.

The repair can happen at another level. Mutated, poorly functioning DNA can be replaced by a better copy if two similar DNA strands line up and are cut and the pieces are exchanged. (Of course, one strand will end up worse than before, too.) That's an advantage that would function at the level of the individual and its offspring.

Recombination could begin as a way to incorporate new DNA sequences (from food) into the genome. I suppose it's even possible that it got started inserting virus-like sequences into genomes. Lots of speculation here.

Laurence A. Moran

Larry Moran is a Professor Emeritus in the Department of Biochemistry at the University of Toronto. You can contact him by looking up his email address on the University of Toronto website.

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Quotations

The old argument of design in nature, as given by Paley, which formerly seemed to me to be so conclusive, fails, now that the law of natural selection has been discovered. We can no longer argue that, for instance, the beautiful hinge of a bivalve shell must have been made by an intelligent being, like the hinge of a door by man. There seems to be no more design in the variability of organic beings and in the action of natural selection, than in the course which the wind blows.Charles Darwin (c1880)Although I am fully convinced of the truth of the views given in this volume, I by no means expect to convince experienced naturalists whose minds are stocked with a multitude of facts all viewed, during a long course of years, from a point of view directly opposite to mine. It is so easy to hide our ignorance under such expressions as "plan of creation," "unity of design," etc., and to think that we give an explanation when we only restate a fact. Any one whose disposition leads him to attach more weight to unexplained difficulties than to the explanation of a certain number of facts will certainly reject the theory.

Charles Darwin (1859)Science reveals where religion conceals. Where religion purports to explain, it actually resorts to tautology. To assert that "God did it" is no more than an admission of ignorance dressed deceitfully as an explanation...

Quotations

The world is not inhabited exclusively by fools, and when a subject arouses intense interest, as this one has, something other than semantics is usually at stake.
Stephen Jay Gould (1982)
I have championed contingency, and will continue to do so, because its large realm and legitimate claims have been so poorly attended by evolutionary scientists who cannot discern the beat of this different drummer while their brains and ears remain tuned to only the sounds of general theory.
Stephen Jay Gould (2002) p.1339
The essence of Darwinism lies in its claim that natural selection creates the fit. Variation is ubiquitous and random in direction. It supplies raw material only. Natural selection directs the course of evolutionary change.
Stephen Jay Gould (1977)
Rudyard Kipling asked how the leopard got its spots, the rhino its wrinkled skin. He called his answers "just-so stories." When evolutionists try to explain form and behavior, they also tell just-so stories—and the agent is natural selection. Virtuosity in invention replaces testability as the criterion for acceptance.
Stephen Jay Gould (1980)
Since 'change of gene frequencies in populations' is the 'official' definition of evolution, randomness has transgressed Darwin's border and asserted itself as an agent of evolutionary change.
Stephen Jay Gould (1983) p.335
The first commandment for all versions of NOMA might be summarized by stating: "Thou shalt not mix the magisteria by claiming that God directly ordains important events in the history of nature by special interference knowable only through revelation and not accessible to science." In common parlance, we refer to such special interference as "miracle"—operationally defined as a unique and temporary suspension of natural law to reorder the facts of nature by divine fiat.
Stephen Jay Gould (1999) p.84

Quotations

My own view is that conclusions about the evolution of human behavior should be based on research at least as rigorous as that used in studying nonhuman animals. And if you read the animal behavior journals, you'll see that this requirement sets the bar pretty high, so that many assertions about evolutionary psychology sink without a trace.

Jerry Coyne
Why Evolution Is TrueI once made the remark that two things disappeared in 1990: one was communism, the other was biochemistry and that only one of them should be allowed to come back.

Sydney Brenner
TIBS Dec. 2000
It is naïve to think that if a species' environment changes the species must adapt or else become extinct.... Just as a changed environment need not set in motion selection for new adaptations, new adaptations may evolve in an unchanging environment if new mutations arise that are superior to any pre-existing variations

Douglas Futuyma
One of the most frightening things in the Western world, and in this country in particular, is the number of people who believe in things that are scientifically false. If someone tells me that the earth is less than 10,000 years old, in my opinion he should see a psychiatrist.

Francis Crick
There will be no difficulty in computers being adapted to biology. There will be luddites. But they will be buried.

Sydney Brenner
An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist

Richard Dawkins
Another curious aspect of the theory of evolution is that everybody thinks he understand it. I mean philosophers, social scientists, and so on. While in fact very few people understand it, actually as it stands, even as it stood when Darwin expressed it, and even less as we now may be able to understand it in biology.

Jacques Monod
The false view of evolution as a process of global optimizing has been applied literally by engineers who, taken in by a mistaken metaphor, have attempted to find globally optimal solutions to design problems by writing programs that model evolution by natural selection.